dataCustomizedPlot: Create data for customized profile plot

In BIONF/PhyloProfile: PhyloProfile

Create data for customized profile plot

Description

Create data for customized profile plot based on a selected list of genes and/or taxa, containing seed protein IDs (geneID), ortholog IDs (orthoID) together with their ncbi taxonomy IDs (ncbiID and abbrName), full names (fullName), indexed supertaxa (supertaxon), values for additional variables (var1, var2) and the aggregated values of those additional variables for each supertaxon (mVar1, mVar2), number of original and filtered co-orthologs in each supertaxon (paralog and paralogNew), number of species in each supertaxon (numberSpec) and the each supertaxon (presSpec).

Usage

dataCustomizedPlot(dataHeat = NULL, selectedTaxa = "all",
    selectedSeq = "all")

Arguments

dataHeat	a data frame contains processed profiles (see ?fullProcessedProfile, ?filterProfileData)
selectedTaxa	selected subset of taxa. Default = "all".
selectedSeq	selected subset of genes. Default = "all".

Value

A dataframe contains data for plotting the customized profile.

Author(s)

Vinh Tran [e-mail]

See Also

filterProfileData

Examples

data("finalProcessedProfile", package="PhyloProfile")
selectedTaxa <- c("Mammalia", "Saccharomycetes", "Insecta")
selectedSeq <- "all"
dataCustomizedPlot(finalProcessedProfile, selectedTaxa, selectedSeq)

BIONF/PhyloProfile documentation built on Dec. 18, 2024, 7:33 a.m.